mirror of
https://github.com/tgorordo/pages.uoregon.edu.git
synced 2026-06-05 14:42:13 -07:00
357 lines
9.4 KiB
Python
357 lines
9.4 KiB
Python
import marimo
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__generated_with = "0.19.11"
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app = marimo.App(width="medium")
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@app.cell
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def _():
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import marimo as mo
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return (mo,)
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@app.cell
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def _():
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import matplotlib, matplotlib.pyplot as plt
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plt.ion()
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return (plt,)
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@app.cell
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def _():
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import numpy as np
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return (np,)
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@app.cell
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def _():
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from skimage import io
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from skimage.filters import threshold_otsu, threshold_local
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return io, threshold_local, threshold_otsu
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@app.cell
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def _(mo):
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from pathlib import Path
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mo.pdf(src=Path("Homework2.pdf"), width="100%", height="50vh")
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return
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@app.cell(hide_code=True)
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def _(mo):
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mo.md(r"""
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## 1. Thresholding
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""")
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return
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@app.cell
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def _(io):
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robert_mapplethrope_calla_lily_1984_png = io.imread("robert-mapplethrope-calla-lily-1984.png", as_gray=True)
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return (robert_mapplethrope_calla_lily_1984_png,)
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@app.cell
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def _(plt, robert_mapplethrope_calla_lily_1984_png):
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fig1, ax1 = plt.subplots()
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p1 = ax1.imshow(robert_mapplethrope_calla_lily_1984_png, cmap="gray")
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fig1.colorbar(p1, ax=ax1)
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fig1
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return
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@app.cell
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def _(robert_mapplethrope_calla_lily_1984_png, threshold_otsu):
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robert_mapplethrope_calla_lily_global_threshold = threshold_otsu(robert_mapplethrope_calla_lily_1984_png)
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robert_mapplethrope_calla_lily_global_threshold # print
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return (robert_mapplethrope_calla_lily_global_threshold,)
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@app.cell
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def _(
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plt,
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robert_mapplethrope_calla_lily_1984_png,
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robert_mapplethrope_calla_lily_global_threshold,
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):
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fig2, (ax2a, ax2b) = plt.subplots(1, 2, figsize=(8, 4))
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ax2a.hist(robert_mapplethrope_calla_lily_1984_png.flatten(), log=True, bins="auto")
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ax2a.vlines(robert_mapplethrope_calla_lily_global_threshold, 0, 80_000, color="r")
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p2b = ax2b.imshow(robert_mapplethrope_calla_lily_1984_png > robert_mapplethrope_calla_lily_global_threshold, cmap="gray")
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fig2.colorbar(p2b, ax=ax2b)
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fig2
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return
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@app.cell
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def _(io, plt):
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fig3, ax3 = plt.subplots()
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istanbul_arch_museum_gray_crop_png = io.imread("istanbul_arch_museum_gray_crop.png", as_gray=True)
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p3 = ax3.imshow(istanbul_arch_museum_gray_crop_png, cmap="gray")
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fig3.colorbar(p3, ax=ax3)
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fig3
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return (istanbul_arch_museum_gray_crop_png,)
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@app.cell
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def _(istanbul_arch_museum_gray_crop_png, threshold_otsu):
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istanbul_global_threshold = threshold_otsu(istanbul_arch_museum_gray_crop_png)
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istanbul_global_threshold # print
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return (istanbul_global_threshold,)
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@app.cell
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def _(istanbul_arch_museum_gray_crop_png, istanbul_global_threshold, plt):
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fig4, (ax4a, ax4b) = plt.subplots(1, 2, figsize=(8, 4))
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ax4a.hist(istanbul_arch_museum_gray_crop_png.flatten(), log=True, bins="auto")
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ax4a.vlines(istanbul_global_threshold, 0, 300_000, color='r')
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p4b = ax4b.imshow(istanbul_arch_museum_gray_crop_png > istanbul_global_threshold, cmap="gray")
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fig4.colorbar(p4b, ax=ax4b)
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fig4
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return
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@app.cell
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def _(io):
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robert_mapplethrope_calla_lily_1984_crop_png = io.imread("robert-mapplethrope-calla-lily-1984_CROP.png", as_gray=True)
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return (robert_mapplethrope_calla_lily_1984_crop_png,)
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@app.cell
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def _(plt, robert_mapplethrope_calla_lily_1984_crop_png):
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fig5, ax5 = plt.subplots()
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p5 = ax5.imshow(robert_mapplethrope_calla_lily_1984_crop_png, cmap="gray")
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fig5.colorbar(p5, ax=ax5)
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fig5
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return
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@app.cell
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def _(robert_mapplethrope_calla_lily_1984_crop_png, threshold_otsu):
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robert_mapplethrope_calla_lily_crop_global_threshold = threshold_otsu(robert_mapplethrope_calla_lily_1984_crop_png)
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robert_mapplethrope_calla_lily_crop_global_threshold # print
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return (robert_mapplethrope_calla_lily_crop_global_threshold,)
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@app.cell
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def _(
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plt,
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robert_mapplethrope_calla_lily_1984_crop_png,
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robert_mapplethrope_calla_lily_crop_global_threshold,
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):
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fig6, (ax6a, ax6b) = plt.subplots(1, 2, figsize=(8, 4))
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ax6a.hist(robert_mapplethrope_calla_lily_1984_crop_png.flatten(), log=True, bins="auto")
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ax6a.vlines(robert_mapplethrope_calla_lily_crop_global_threshold, 0, 80_000, color="r")
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p6b = ax6b.imshow(robert_mapplethrope_calla_lily_1984_crop_png > robert_mapplethrope_calla_lily_crop_global_threshold, cmap="gray")
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fig6.colorbar(p6b, ax=ax6b)
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fig6
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return
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@app.cell(hide_code=True)
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def _(mo):
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mo.md(r"""
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## 2. Thresholding, again
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""")
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return
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@app.cell
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def _(
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istanbul_arch_museum_gray_crop_png,
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plt,
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robert_mapplethrope_calla_lily_1984_crop_png,
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robert_mapplethrope_calla_lily_1984_png,
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threshold_local,
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):
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fig7, (ax7a, ax7b, ax7c) = plt.subplots(1, 3, figsize=(12, 4))
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p7a = ax7a.imshow(robert_mapplethrope_calla_lily_1984_png > threshold_local(robert_mapplethrope_calla_lily_1984_png, block_size=123), cmap="gray")
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fig7.colorbar(p7a, ax=ax7a)
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p7b = ax7b.imshow(istanbul_arch_museum_gray_crop_png > threshold_local(istanbul_arch_museum_gray_crop_png, block_size=123), cmap="gray")
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fig7.colorbar(p7b, ax=ax7b)
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p7c = ax7c.imshow(robert_mapplethrope_calla_lily_1984_crop_png > threshold_local(robert_mapplethrope_calla_lily_1984_crop_png, block_size=123), cmap="gray")
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fig7.colorbar(p7c, ax=ax7c)
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fig7
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return
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@app.cell(hide_code=True)
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def _(mo):
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mo.md(r"""
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## 3. Protein density
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""")
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return
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@app.cell
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def _(io, plt):
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fig8, ax8 = plt.subplots()
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microarray_crop_png = io.imread("microarray_crop.png", as_gray=True)
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p8 = ax8.imshow(microarray_crop_png, cmap="gray")
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fig8.colorbar(p8, ax=ax8)
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fig8
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return
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@app.cell(hide_code=True)
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def _(mo):
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mo.md(r"""
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## 4. Non-uniform background subtraction
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""")
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return
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@app.cell
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def _(io, plt):
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fig9, ax9 = plt.subplots()
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GUV24_bead_crop_png = io.imread("GUV24_bead_Crop.png", as_gray=True)
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p9 = ax9.imshow(GUV24_bead_crop_png, cmap="gray")
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fig9.colorbar(p9, ax=ax9)
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fig9
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return (GUV24_bead_crop_png,)
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@app.cell
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def _(GUV24_bead_crop_png, np):
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x = np.arange(GUV24_bead_crop_png.shape[0])
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y = np.arange(GUV24_bead_crop_png.shape[1])
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xs, ys = np.meshgrid(x, y)
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return x, xs, ys
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@app.cell
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def _(GUV24_bead_crop_png, plt, xs, ys):
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fig10, ax10 = plt.subplots()
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ax10 = plt.axes(projection ='3d')
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p10 = ax10.plot_surface(xs, ys, GUV24_bead_crop_png, cmap="viridis")
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fig10
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return
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@app.cell(hide_code=True)
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def _(mo):
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mo.md(r"""
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### b.
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""")
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return
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@app.cell
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def _(GUV24_bead_crop_png, np, xs):
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w = np.vstack([xs.ravel(), np.ones(xs.size)]).T
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mx, c = np.linalg.lstsq(w, GUV24_bead_crop_png.ravel())[0] # (c-410) 3pt alternative
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(mx, c)
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return c, mx
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@app.cell
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def _(GUV24_bead_crop_png, c, mx, plt, x, xs, ys):
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fig11, (ax11a, ax11b) = plt.subplots(1, 2, figsize=(8, 4))
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ax11a.plot(x, mx * x + c, c='r')
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ax11a.scatter(xs.ravel(), GUV24_bead_crop_png.ravel(), s=4)
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ax11b.scatter(ys.ravel(), GUV24_bead_crop_png.ravel(), s=4)
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fig11
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return
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@app.cell(hide_code=True)
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def _(mo):
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mo.md(r"""
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### c.
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#### 410:
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""")
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return
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@app.cell
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def _(GUV24_bead_crop_png, np, xs, ys):
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# z = m @ w + c
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w2 = np.vstack([xs.ravel(), ys.ravel(), np.ones(GUV24_bead_crop_png.size)]).T
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mx2, my2, c2 = np.linalg.lstsq(w2, GUV24_bead_crop_png.ravel())[0]
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(mx2, my2, c2)
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return c2, mx2, my2
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@app.cell
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def _(GUV24_bead_crop_png, c2, mx2, my2, plt, xs, ys):
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fig12, ax12 = plt.subplots()
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ax12 = plt.axes(projection ='3d')
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ax12.plot_surface(xs, ys, GUV24_bead_crop_png, cmap="viridis", alpha=0.3)
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ax12.plot_surface(xs, ys, mx2 * xs + my2 * ys + c2, cmap="plasma")
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fig12
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return
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@app.cell
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def _(GUV24_bead_crop_png, c2, mx2, my2, plt, xs, ys):
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fig13, ax13 = plt.subplots()
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ax13 = plt.axes(projection ='3d')
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ax13.plot_surface(xs, ys, GUV24_bead_crop_png - (mx2 * xs + my2 * ys + c2), cmap="viridis")
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fig13
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return
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@app.cell
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def _(GUV24_bead_crop_png, c2, mx2, my2, plt, xs, ys):
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fig14, ax14 = plt.subplots()
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p14 = ax14.imshow(GUV24_bead_crop_png - (mx2 * xs + my2 * ys + c2), cmap="gray")
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fig14.colorbar(p14, ax=ax14)
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fig14
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return
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@app.cell(hide_code=True)
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def _(mo):
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mo.md(r"""
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#### 510:
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""")
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return
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@app.cell
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def _(GUV24_bead_crop_png, np, xs, ys):
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# z = m @ w + c
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w3 = np.vstack([xs.ravel(), np.square(xs.ravel()),
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ys.ravel(), np.square(ys.ravel()),
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np.ones(GUV24_bead_crop_png.size)]).T
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mx3, mx3x, my3, my3y, c3 = np.linalg.lstsq(w3, GUV24_bead_crop_png.ravel())[0]
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(mx3, mx3x, my3, my3y, c3)
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return c3, mx3, mx3x, my3, my3y
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@app.cell
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def _(GUV24_bead_crop_png, c3, mx3, mx3x, my3, my3y, np, plt, xs, ys):
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fig15, ax15 = plt.subplots()
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ax15 = plt.axes(projection ='3d')
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ax15.plot_surface(xs, ys, GUV24_bead_crop_png, cmap="viridis", alpha=0.3)
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ax15.plot_surface(xs, ys, mx3 * xs + mx3x * np.square(xs) + my3 * ys + my3y * np.square(ys) + c3, cmap="plasma")
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return
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@app.cell
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def _(GUV24_bead_crop_png, c3, mx3, mx3x, my3, my3y, np, plt, xs, ys):
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fig16, ax16 = plt.subplots()
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p16 = ax16.imshow(GUV24_bead_crop_png - (mx3 * xs + mx3x * np.square(xs) + my3 * ys + my3y * np.square(ys) + c3), cmap="gray")
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fig16.colorbar(p16, ax=ax16)
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fig16
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return
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@app.cell
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def _(GUV24_bead_crop_png, c3, mx3, mx3x, my3, my3y, np, plt, xs, ys):
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fig17, ax17 = plt.subplots()
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ax17 = plt.axes(projection ='3d')
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ax17.plot_surface(xs, ys, GUV24_bead_crop_png -
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(mx3 * xs + mx3x * np.square(xs) + my3 * ys + my3y * np.square(ys) + c3), cmap="viridis")
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return
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@app.cell
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def _():
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return
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if __name__ == "__main__":
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app.run()
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